conduitR is an R package for metaproteomics: the large-scale identification and quantification of proteins from microbial communities (e.g. gut microbiome, soil, bioreactors). It provides a single, consistent toolkit for building search databases, processing DIA-NN output, linking proteins to taxonomy and function, and running differential analysis and visualizations.
The package powers Conduit (a Snakemake workflow for metaproteomics) and Conduit-GUI (a graphical interface to explore Conduit results), but you can use conduitR on its own for custom pipelines and analyses.
QFeatures object (precursors → peptides → protein groups) with assay links.QFeatures object with precursors, peptides, and protein groups.QFeatures from sample annotations and multiple count matrices.scale_color_conduit_d, scale_fill_conduit_c, set_plot_theme, etc.).%!in% operator; integration with existing R workflows.Install the development version from GitHub:
After installation, load the package and try a few entry points:
library(conduitR)
# Check that the UniProt API is reachable (required for downloads)
check_api_service()
# Validate UniProt IDs (no network needed)
validate_uniprot_accession_ids(c("P12345", "invalid_id", "A0A023GPI8"))
# Convert a DIA-NN parquet report to QFeatures (requires a local file)
# qf <- diann_to_qfeatures("path/to/report.parquet")
# plot_features_per_sample(qf, assay = "protein_groups")
# Run differential analysis (after building design/contrast)
# terms <- find_possible_contrast_terms(qf, "protein_groups", ~ group)
# res <- perform_limma_analysis(qf, "protein_groups", ~ group, "treatmentB - treatmentA")
# plot_volcano(res$top_table)Function help and examples are in the built-in documentation: e.g. ?get_fasta_file, ?diann_to_qfeatures, ?perform_limma_analysis.
Core dependencies include QFeatures (proteomics data structures), limma (differential expression), SummarizedExperiment, Biostrings, httr2, KEGGREST, rentrez, tidyr, dplyr, ggplot2, plotly, metacoder, arrow, and others for specific features. See the DESCRIPTION file for the full list.
?function_name for any exported function; many have runnable or \dontrun examples.MIT License; see LICENSE for details.